Variant rs12447486 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000525377.6(IL32):c.339+4042G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 147,240 control chromosomes in the GnomAD database, including 19,744 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.51 ( 19744 hom., cov: 29)

Consequence

IL32
ENST00000525377.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.232

Variant links:

Genes affected

IL32 (HGNC:16830): (interleukin 32) This gene encodes a member of the cytokine family. The protein contains a tyrosine sulfation site, 3 potential N-myristoylation sites, multiple putative phosphorylation sites, and an RGD cell-attachment sequence. Expression of this protein is increased after the activation of T-cells by mitogens or the activation of NK cells by IL-2. This protein induces the production of TNFalpha from macrophage cells. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

IL32 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.3072281G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL32	ENST00000525377.6 linkuse as main transcript	c.339+4042G>A		intron_variant		5		ENSP00000433866.3		E9PIV2

Frequencies

GnomAD3 genomes

AF:

0.508

AC:

74733

AN:

147128

Hom.:

19740

Cov.:

show subpopulations

Gnomad AFR

AF:

0.282

Gnomad AMI

AF:

0.757

Gnomad AMR

AF:

0.488

Gnomad ASJ

AF:

0.587

Gnomad EAS

AF:

0.388

Gnomad SAS

AF:

0.586

Gnomad FIN

AF:

0.634

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.629

Gnomad OTH

AF:

0.521

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.508

AC:

74769

AN:

147240

Hom.:

19744

Cov.:

AF XY:

0.508

AC XY:

36542

AN XY:

71912

show subpopulations

Gnomad4 AFR

AF:

0.282

Gnomad4 AMR

AF:

0.488

Gnomad4 ASJ

AF:

0.587

Gnomad4 EAS

AF:

0.388

Gnomad4 SAS

AF:

0.586

Gnomad4 FIN

AF:

0.634

Gnomad4 NFE

AF:

0.629

Gnomad4 OTH

AF:

0.522

Alfa

AF:

0.415

Hom.:

967

Asia WGS

AF:

0.465

AC:

1620

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.8

DANN

Benign

0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over